UCSB

Apr 15-16, 2016

9:00 am - 4:30 pm

Instructors:
Remi Daigle, Julie Stewart Lowndes, Ben Best

Helpers:
Jamie Afflerbach, Casey O'Hara, Grant McDermott, Dan Ovando

General Information

Software Carpentry's mission
is to help scientists and engineers get more research done in less
time and with less pain by teaching them basic lab skills for
scientific computing. This hands-on workshop will cover basic
concepts and tools, including program design, version control, data
management, and task automation. Participants will be encouraged to
help one another and to apply what they have learned to their own
research problems.

Requirements: Participants must bring a laptop with a
Mac, Linux, or Windows operating sytem (not a tablet, Chromebook, etc.) that they have administrative privileges
on. They should have a few specific software packages installed (listed
below). They are also required to abide by
Software Carpentry's
Code of Conduct.

Windows

Select "Use Git from the Windows Command Prompt" and click on "Next".
If you forgot to do this programs that you need for the workshop will not work properly.
If this happens rerun the installer and select the appropriate option.

Mac OS X

The default shell in all versions of Mac OS X is Bash, so no
need to install anything. You access Bash from the Terminal
(found in
/Applications/Utilities). You may want to keep
Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your
machine is set up differently you can run it by opening a
terminal and typing bash. There is no need to
install anything.

Git and Github Desktop app

Git is a version control system that lets you track who made changes
to what when and has options for easily updating a shared or public
version of your code
on github.com. You will need a
supported
web browser (current versions of Chrome, Firefox or Safari,
or Internet Explorer version 9 or above). The Github Desktop app is an easy to use interface for using Git locally and communicating with github.com.

Windows

Git should be installed on your computer as part of your Bash
install (described above). Also, please install the
Github Desktop app.

Mac OS X

For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
this list.
After installing Git, there will not be anything in your /Applications folder,
as Git is a command line program. Also, please install the
Github Desktop app.
For older versions of OS X (10.5-10.8) use the
most recent available installer labelled "snow-leopard"
available here. Also, please install the
Github Desktop app.

Linux

If Git is not already available on your machine you can try to
install it via your distro's package manager. For Debian/Ubuntu run
sudo apt-get install git and for Fedora run
sudo yum install git. Also, please install the
Github Desktop app.

Text Editor

When you're writing code, it's nice to have a text editor that is
optimized for writing code, with features like automatic
color-coding of key words. The default text editor on Mac OS X and
Linux is usually set to Vim, which is not famous for being
intuitive. if you accidentally find yourself stuck in it, try
typing the escape key, followed by :q! (colon, lower-case 'q',
exclamation mark), then hitting Return to return to the shell.

Windows

nano is a basic editor and the default that instructors use in the workshop.
To install it,
download the Software Carpentry Windows installer
and double click on the file to run it.
This installer requires an active internet connection.

Others editors that you can use are
Notepad++ or
Sublime Text.
Be aware that you must
add its installation directory to your system path.
Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop.
It should be pre-installed.

Mac OS X

Linux

You can download the binary files for your distribution
from CRAN. Or
you can use your package manager (e.g. for Debian/Ubuntu
run sudo apt-get install r-base and for Fedora run
sudo yum install R). Also, please install the
RStudio IDE.